Biochem - Lecture 3 Learning Objectives

all of the learning objectives and key concepts for the third lecture on amino acids, linked functions, and peptide bonds

primary protein structure

sequence of amino acids in protein

secondary protein structure

folds up into shapes

tertiary protein structure

whole structure of protein

quaternary protein structure

multiple proteins

amino acid residue

amino acid that is attached by a peptide bond to another amino acid

backbone

the amino group, the carboxyl group, and the alpha carbon

side chains

the R group unique to each amino acid

disulfide bonds

also known as disulfide bridges. covalent bonds that form between the sulfur atoms of two cysteine amino acids in proteins

conformation

the folded shape of the protein as determined by the amino acid sequence

configuration

L or D. Most amino acids are L-isomers

What is the difference between glutamate and glutamic acid?

glutamic acid has no charges and no net charge but if it undergoes a protonation-deprotonation reaction, it will produce glutamate, which contains multiple charges on it (same is true for other acids)

-ate means what?

conjugate base form of a carboxylic acid

what are linked functions?

reactions that work together to maintain a cellular process

peptide bond

chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule

when does deprotonation occur?

when the compound is more acidic

when does protonation occur?

when the compound is more basic

what ionizable functional groups will deprotonate?

carboxyl group

what ionizable functional groups will protonate?

amino group

what amino acids deprotonate?

D, E, Y, R

What amino acids protonate?

H, K, C

what is the product of condensation of 2 amino acids?

dipeptide, which is a molecule formed by joining two amino acids through a peptide bond

if pKa < pH the compound will

deprotonate

if pKa > pH the compound will

protonate

if pKa = pH the compound will

be equal parts protonated and deprotonated

amino acids are ionizable because

their side chains can gain or lose electrons

what pH are we using?

physiological pH = 7

alpha carbonyl group will be

deprotonated

alpha amino group will be

protonated

aspartate (aspartic acid) will be

deprotonated

glutamate (glutamic acid) will be

deprotonated

histidine will be

deprotonated

cysteine will be

protonated

lysine will be

protonated

tyrosine will be

protonated

arginine will be

protonated